"There's a growing body of science indicating that the pesticides are a key factor in recent global bee deaths," said Lisa Archer, director of the food and technology program at the environmental group, Friends of the Earth.

Archer said her group, which is leading the petition effort, tested plants for sale at Lowe's and Home Depot and more than half had the pesticides. She said because there were no labels on the plants or pesticides that they could be harmful to bees, consumers were left in the dark about the dangers.

Home Depot was aware of the pesticide issue before the petition effort began, said Ron Jarvis, vice president of merchandising and sustainability at the retailer.

"We've been in contact for months with several environmental groups about neonicotinoids," Jarvis told CNBC by phone. "Now we've been in contact with Friends of the Earth."

Jarvis said Home Depot has been working on an alternative to neonicotinoids for some time and several of the retailer's suppliers are already using the replacements.

Lowe's has not made any public statements or responded to meeting requests from Friends of the Earth, said Archer. (Calls to the company's corporate offices were not returned in time for this story.)